Pokemon: The Shadow Flames
by GreenSonic21
Summary: Sequel to "HG&SS Quest!" Hareta returns to Sinnoh after his adventures in Johto and Kanto, but his time at home is about to be cut short by the return of two old enemies. And that's just the beginning of his problems... Rating may change. ON HIATUS.
1. A Champion's Welcome Home

Hey guys! Well, as you can tell, this is the beginning of the sequel to "Pokémon HeartGold and SoulSilver Quest!" that I mentioned. This first chapter isn't all that amazing since it's the beginning and I spent most of it setting up future events, but it's all right.

I'm still going to write my other stories, but I just wanted to put something down for this so I can start working things out. I know what the major events are going to be. I just need to figure out what I want to happen in between the events. So the next chapter is probably going to be a filler to keep from jumping into the action too quickly, but we'll see. I'll try to keep it good.

Anyway, on with the show.

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><p>Out on the sea, some ways away from Canalave City, a ship swiftly cut across the water as it neared the end of its journey. On the deck of the ship, Hareta stepped outside and stretched out his arms while inhaling the fresh ocean air. "Mm… The air tastes good today. I can't wait to get home!" he said to himself. He let his arms drop to his sides and then made his way towards the bow of the ship, where he rested his arms on the railing while he waited for the ship's destination to show up in the distance.<p>

It had been several days since he parted ways with Gold and Kotone back in Cherrygrove City and he couldn't wait to see everyone back home again. He and his Pokémon friends had managed to keep themselves entertained during the trip, but now they were ready to get back on dry land. Hareta had already gathered everything up in his backpack, which he was currently wearing, and now was trying to keep his patience in check until the ship reached Canalave City.

Soon enough, the port city appeared on the horizon, the sight of it exciting Hareta as he realized it wouldn't be long now. The ship passed under the drawbridge as it entered the canal, coming to a stop at an empty dock. No longer able to wait, Hareta dashed over to the right side of the ship and leapt over the railing, the gray pavement below rushing up to meet him.

He landed on his feet, stood up straight, and held out his arms as he said, "It feels so good to be back in Sinnoh again!" Aside from freaking out a little when he leapt over the side of the ship, none of the sailors near the ship really seemed to pay him any attention, but he didn't care. He left the pier as the other passengers began pouring off of the ship, trying to keep his excitement in check as he thought about seeing Mitsumi, Jun, Professor Rowan, and his parents again.

As he made his way through the city, Hareta noticed Byron's Gym off on the side of the road he was walking on. He came to a stop and said to himself, "It's been a while since I've seen Byron, come to think of it. I wonder if he's in right now." He walked off the main road and headed towards the Gym, only to be dismayed when he found a sign on the Gym doors saying that it was closed for the day. "Oh well, maybe next time," he muttered as he walked away, returning to the road and walking past the Canalave Library.

While walking towards the gate leading towards Route 218, Hareta noticed the drawbridge rising up and turned his head to watch a ship leave. While he was distracted, he accidentally walked into somebody in front of him, bouncing back a bit due to bumping into something that seemed to jiggle on contact. Hareta quickly turned his head forward and apologized, "Oops! Sorry…"

The man in front of him replied, "That's all right. Just watch where you're going next time."

Hareta immediately recognized that voice and took a second look, at which point he realized that the man had a swollen behind, sea green hair, and was wearing a futuristic-looking uniform. Even from behind, he knew who it was. "Hey! You're B-2!"

The man noticeably flinched at that and turned his head to look over his shoulder, saying, "What the…? Hareta?" He quickly spun around, revealing that he had been looking at a laptop in his arms, and said, "I wasn't looking at anything evil or suspicious, I swear! I've turned over a new leaf since we last saw each other! You've got nothing on me!"

Hareta looked back at him blankly for a moment before he said, "I just wanted to say hi."

B-2 straightened up, presumably because he felt relieved that Hareta didn't think he was up to something, and replied, "Oh. Hello. Did you just get back from Johto? Commander Saturn told me you beat him in the Silver Conference."

Hareta nodded, "Yeah. I didn't expect to see him in a competition like that." He then asked, "Hey, how's your butt feeling?"

B-2 answered, "Uh, fine I guess. It hasn't really changed much since you bit it."

Hareta nervously ran a hand through the back of his hair as he said, "Yeah, uh… Well, I was just thinking maybe I could do something about that. You know, try to get it back to the way it was for you?"

B-2 raised an eyebrow at that, "That would be nice, but I don't see what you could do to help. I've tried to do something about it, but nothing I've tried has had any effect."

Hareta said, "Well, let me try something I've been working on. If it does what I think it will, I should only have to do it this one time."

B-2 looked at him oddly for a few moments before sighing, "Okay, I'll give whatever it is a shot. What do I have to do?"

Hareta replied, "Nothing. Let's just go in the forest where no one will see us." Although he was now really suspicious of whatever Hareta was planning, he agreed and closed his laptop before they ducked into the line of trees along the side of the road.

A few minutes later, B-2 was squatting in the middle of a clearing with Hareta standing right behind him. The young Trainer was doodling with his fingers and hands while looking down at the former Galactic Grunt's hindquarters. B-2 once tried to look over his shoulder at Hareta, only to have the boy say, "Face forward!"

B-2 complied, but he asked, "Look, would you mind telling me what you're going to do? And why do I have to be in this position?"

Hareta replied, "Because this might be a bit sudden and I don't want you to fall over. Just relax; at worst, this'll only hurt for a second." With that, he bent his knees slightly, bringing himself closer to B-2, and held his hands over his buttocks. He then focused, blue flames beginning to envelope his hands as he projected his Aura into them.

B-2 gave a sharp gasp when he felt Hareta grab him and yelled, "Hey, what do you think you're…" He stopped in mid-sentence as he felt a warm heat begin to flow through his body, though it was mostly centered on his swollen rear. "Hey… that feels really nice," he murmured.

Hareta nodded, "That's good. That means I'm doing it right. Just stay put and it'll be over before you know it." B-2 nodded dumbly, his mind relaxing from the warm sensation he was feeling. About a minute later, Hareta lifted his hands off of B-2's butt and dashed away, calling back, "There you go! See you later!"

B-2 snapped out of his haze at that and turned his head to see Hareta running towards the line of trees that led to Route 218. "Hey, wait!" he exclaimed, standing up and running after him, albeit slightly awkwardly as he realized that something seemed to be off, but that wasn't important right now. As he stepped out onto Route 218, he looked to the left to see Hareta surfing away on his Empoleon. "Ugh! What a weird kid!" B-2 muttered, placing his hands on his hips. At that moment, he realized why he had felt so awkward running earlier.

Looking back over his shoulder, he realized that his swollen posterior was no longer swollen! It was back to the same size it had been before Hareta had bitten him! "I… I don't believe it! It's back to normal!" B-2 exclaimed. Before he could get too excited, he remembered that he had no idea what Hareta had done to return it to the way it used to be. He glanced to the east, towards Jubilife City, and muttered, "What did he do just now…?"

After reaching the eastern end of Route 218, Hareta thanked Empoleon and returned him to his Poké Ball before moving onto Jubilife City. Although he took his time navigating the streets of the city, nobody offered him more than a passing glance as he walked past, which he was thankful for. He didn't win the Silver Conference just to get attention after all. He soon headed south out of the city, leaping down the ledges on Route 202 as he made his way to Sandgem Town.

As soon as he arrived in Sandgem Town, Hareta headed for Professor Rowan's lab. He knocked on the front door while calling, "Hey Gramps, it's me! I'm home!" He stopped knocking after a minute and got confused when it seemed like no one was coming to answer the door. He placed a hand on the doorknob and turned it, only to find that it was locked. Worried, Hareta walked around the lab while peering through the windows, but it didn't appear anyone was inside.

Hareta stood near the side of the lab that was closest to Route 201, scratching his head as he wondered, "Where is everybody? Mitsumi told me that Gramps sometimes goes out to buy sweets, but I thought he kept a bunch in his refrigerator." While he was lost in thought, he suddenly heard a familiar sound behind him and turned to see a group of Aipom and Bidoof coming towards him. He smiled and ran over to them, giving them all a big hug and saying, "Hey guys! It's so good to see you again!" After a minute, he let them go and asked, "Hey, has anyone seen Gramps today?"

One of the Aipom said, "(Ooh ooh! We saw him earlier! He was heading down Route 201!)"

A Bidoof nodded, "(Uh-huh! He was probably going to visit your parents! That was a while ago and he still hasn't come back, so that must be what he's doing!)"

Hareta smiled, "Oh good! I was starting to get a little worried that something bad had happened."

The Aipom tugged on Hareta's arm and said, "(Come on, Hareta! Come and play with us again and tell us about your newest adventure! Everyone's been waiting to see you again!)"

Hareta stood up and replied, "Okay! Just give me a second." He then backed up a step and stripped down to his shorts. He then took his Poké Balls out of his backpack and shoved his clothes into it for safekeeping. Hareta then called out his Pokémon while slinging his backpack over a shoulder and, after telling them what was going on, they all followed the Aipom and Bidoof into the forest. It was time to kick back after a long journey and have some fun.

Hours later, as the sun was beginning to set in the west, Hareta exited the forest fully clothed with Minun and Sneasel on his shoulders, the three of them waving to all of Hareta's forest friends as they headed for Twinleaf Town. It was a great time for everyone involved; Typhlosion, Sceptile, Scizor, and Sneasel were all happily welcomed by Hareta's friends and, along with Hareta's other Pokémon, got to have a little fun around the forest. Hareta had some fun too, though he spent quite a bit of time talking about his journey through Johto and Kanto, filling everyone in on everything that had happened. But now it was time for them to go and check in with the boy's parents and spend the evening with them.

Soon after reaching the town, Hareta broke out into a run as his excitement began to peak once again. When he reached the fence in front of his house, he found Kaisei, Plusle, and Johanna waiting out front. "Mom! Dad! Plusle!" he exclaimed as he leapt over the fence and ran over to them, Kaisei scooping his flesh and blood up in a big hug while Plusle and Minun hugged and Sneasel leapt into Johanna's arms, the mother squeezing Hareta into the hug after Kaisei set him back down.

"Hey, there's my boy! We heard from Professor Rowan that you'd probably be back sometime today!" Kaisei exclaimed.

After Johanna released him, Hareta said, "So you decided to wait out front for me!"

Mitsumi stepped out onto the porch, Jun, Professor Rowan, and Byron behind her, and spoke, "Well, the noise coming from the forest helped with the timing. As soon as it quieted down, we figured you would be showing up soon."

Hareta giggled, "You can read me like a book, can't you, Mitsumi?"

Jun grinned, "Heh, I wouldn't go that far, Hareta. If she could read you that good, nothing you do would come as a surprise to her. Still, she's got part of you figured out, and that's saying something."

Mitsumi glanced back at him and smirked, "Yeah, unlike you. You've got a long way to go."

Professor Rowan stepped forward and said, "Welcome home, Hareta. It's been so long since I last saw you. It's good to see you again."

Hareta ran over to him and gave him a hug, which the professor returned, saying, "It's so good to see you again too, Gramps!"

Byron walked up beside Hareta and slid a hand under the boy's hat, ruffling his hair as he said, "Ha ha! A real fighter when the going gets tough, yet a real softie when things are peaceful! You're still something else, Hareta!" After Hareta let go of Professor Rowan, Byron said, "I hope you brought your appetite! We've got steaming hot Chinese food in the kitchen, just like Mitsumi said you wanted!"

Hareta grinned, "Sweet! I'm starving!" As they went inside, everyone gave a laugh at that.

As everyone, along with their Pokémon, dug into their food, Hareta filled them in on what he had been doing with Gold and Kotone after parting ways with Mitsumi and Jun. He mentioned the little adventure they had had while climbing Mt. Silver, the Triple Battle in Cherrygrove City, and, of course, meeting Red.

"No way! THE Red? The guy who supposedly brought down Team Rocket and then became the Kanto Champion three years ago?" Jun asked.

"Uh-huh! I first met him after I won the Silver Conference. He told me that if I could earn the right to climb Mt. Silver, he'd battle me. And he sure kept his promise!" Hareta replied.

"So you got to battle a three year veteran Trainer and happened to get a chance sighting of the legendary Moltres… Hm, I'm starting to see why you wanted to stay in Johto for a little while longer," Mitsumi joked. Hareta nodded at that.

Jun asked, "So who won?"

Hareta looked back at him, confused. "Huh?"

Jun repeated, "Who won the battle? You or Red?"

Hareta looked back at him for a moment before saying, "Jun, don't sweat the details." The blonde Trainer raised an eyebrow at that, clearly confused.

Professor Rowan spoke, "I suppose who won or lost is not what's important in the long run. The point is that you got to meet and battle an exceptionally strong Trainer, correct?" Hareta nodded.

Byron grinned, "Hey, well said, professor! I know if I ever got the chance to battle a Trainer like that, I'd want to take it too! No matter the outcome, it would definitely be an awesome experience!" As everyone continued eating, the kitchen's air was filled with idle conversation, Kaisei and Johanna talking about what had been happening in Twinleaf Town lately, Byron mentioning how tough his Fortress of Steel was for challengers and that he'd like to see Hareta challenge it again, and Professor Rowan discussing some of his research.

At the end of the meal, Johanna said, "Don't forget your fortune cookies, everyone! And remember, it's not the kind of cookie you eat, Hareta." The raven haired Trainer just giggled at that.

While the adults simply read their fortunes with a mild curiosity, Hareta, Jun, and even Mitsumi looked a little more excited at finding out what their fortunes were. Jun broke his open first and read the slip of paper inside. 'Good things come to those who wait. Remain patient and you will find that which you dream about most.' Jun grinned slightly to himself at that. That had to mean good things for him and Mitsumi.

Unfortunately, Mitsumi's fortune didn't hold a similar message, at least not one that she was particularly excited about. 'The road that you face may be broken apart by unearthed secrets. Be patient and be willing to accept that some things are meant to change.' She glared slightly at the words. "_What is that supposed to mean?_" she wondered.

She looked over at Hareta a moment later. He had a worried look on his face as he read his fortune. 'Disharmony will reveal itself soon. A strong mind will be essential during dire times.' After watching him for a moment, Mitsumi reached over and took the slip of paper out of his hands, crumpling it up as she said, "Don't look so worried, Hareta. Whatever your fortune is, it probably doesn't mean anything."

Hareta started, "But it said…"

Mitsumi interrupted, "They all say something. But it's nothing to freak out over. Just because a cookie says something about your future doesn't mean it's going to happen."

Hareta protested, "But cookies are delicious! Why would they lie?"

Professor Rowan chuckled, then reached a hand over the table and placed it on Hareta's shoulder, saying, "Hareta, Mitsumi is right. There's nothing wrong with thinking that a prediction of the future may be right, but don't let it control your life. That can mean a lot of things for your future, and not all of them are particularly good possibilities to consider. The future is always in motion; what will happen is never completely set in stone."

Hareta gave a small smile at that, "Okay, Gramps. I won't obsessively worry about it."

Byron smiled, "That's the spirit, Hareta! Don't put all your faith in some scrap of paper that was probably picked at random from a barrel in the back of the kitchen. Make your own future!"

**Meanwhile…**

A man sat behind a desk in a room that had metal walls and a metal floor, examining a knife in his hands. He wore a lab coat over a Team Galactic Commander uniform, glasses that had red lenses, and he had mauve hair and brown eyes. It was Charon, a former commander of Team Galactic and the former leader of Neo Team Galactic before the International Police arrested him. At the thought of what led to his capture, he let out a yell and threw the knife towards the wall on the other side of the room.

The knife ended up hitting a crudely made 'WANTED' poster that had Hareta's picture on it, landing squarely on one of the boy's eyes. His was not the only poster on the wall; to the right of the poster were similar posters of Mitsumi, Jun, Koya, Cyrus, Saturn, Mars, Jupiter, Kaisei, and Looker. All Charon's enemies, all of them apparently having been used for target practice, though Hareta's poster was in the worst shape. It was amazing that it hadn't fallen apart yet, given the number of tears in the picture.

Standing up, Charon walked over to the wall and removed the knife from the wall, glaring at Hareta's picture afterwards. "Enjoy your 'fun' and 'friendship' while you can, Hareta. The day I take my revenge on you is coming soon," he scowled. Turning away a moment later, he headed for a pair of mechanical doors, muttering, "I need to get a status report from the doctor."

**Dr. Mephiles' room**

The doctor stood before his computer console, having a conversation with a mysterious contact in the pitch black room. "We shall see. What is your contingency plan?" the doctor was saying.

The one on the other end answered, "It involves the other god. And I do not believe it will be necessary. While there is one who seeks to stop this plan, his companion is lost and without his memories. In addition, it seems someone has followed them to preserve that which they originated from. I see no reason to intervene."

Dr. Mephiles replied, "Good. They are not like the ones I seek revenge against; they should be easily taken care of." After a moment's pause, he spoke again, "I must cut this meeting short. It appears I have a few matters to take care of." With that, he pressed a button, ending the conversation. The room returned to total darkness, which was interrupted a few moments later when the room's mechanical doors slid open. Dr. Mephiles turned to see Charon standing in the doorway and calmly said, "Ah, my liege. To what do I owe this unexpected pleasure?"

Charon reached over and flicked on the light switch, illuminating the room. He then walked towards Dr. Mephiles, looking up at him as he said, "Don't try to sweet talk me, doctor. What's the status of my new airship?"

Dr. Mephiles turned back to his console and pressed a few keys on it. Moments later, a large helicopter-like airship was displayed on the screen, Charon moving to get a better look at it. Dr. Mephiles spoke, "It is nearing completion, master. The workforce has already finished constructing it; all that remains is to make sure all the systems onboard are functioning properly."

Charon asked, "How soon will it be ready?"

Dr. Mephiles answered, "I would say within the next few days."

Charon nodded, "Good. I already have my revenge planned out and I want to get on with it as soon as possible. And you need to find time to take a shower; every time I see you, you smell like something that crawled out of the depths of the earth." Dr. Mephiles offered no reply to that, so Charon asked, "By the way, what's the status on my new weapon?"

Dr. Mephiles crossed his fingers together as, under his hood, he coldly smiled, "I'm so glad you asked, master. For all the difficulty it presented in being captured, it was surprisingly easy to create a binding armor to ensure total control. I have already finished construction on the armor and am ready to put it to the test. Perhaps you'd like to see it again?"

Charon glanced over at him and replied, "Yes. Show me!" At that command, Dr. Mephiles uncrossed his fingers and held a finger over a red button on the console. He pushed the button and looked to the side as part of the floor slid to the side and a large liquid-filled tube rose up into the room. Charon sported a wide grin as he looked at what it contained.

Floating in the light blue liquid in the middle of the tube was a humanoid, feline-like Pokémon. It had a grayish-purple body with a purple underside, a long purple tail, two short ears, three circular digits on its hands, and a tube extending from the back of its skull to its spine. It was one of the first Pokémon ever created by science: the Genetic Pokémon, Mewtwo.

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><p>Okay, so about this chapter.<p>

I know B-2's swollen butt is his defining aspect, but it seemed more like a way to identify him among all the other Galactic Grunts that appeared in the manga. There won't be any other Galactic Grunts here and I don't plan on doing a lot of butt jokes, so I thought I'd set him right. I'll still try to make him funny, though.

I made an MGS3 reference when Hareta and Jun were talking about the battle with Red. I suppose I should have a decisive outcome in my head, but I'm still worried I'll upset somebody. Maybe I'm just paranoid.

And now we see all those hints I dropped during "HG&SS Quest" starting to show themselves. Just a quick warning: some parts of this story might get a little darker than I normally go for. I know you're probably all sick of me saying that, but it could really happen this time.

Okay, that's enough out of me. See you later!


	2. Teacher and Student

Hareta stepped out the front door of his parents' house, swinging the left strap of his backpack over his shoulder as he called back into the house, "I'm going to visit Gramps, mom! I'll be back later!"

Johanna called back from the kitchen, "All right, dear! See if you can convince your father to come home while you're there! He skipped out on doing the dishes last night; it's definitely his turn tonight!"

Hareta giggled and said, "I'll try, mom!" He then closed the door and reached into the pockets of his jacket, pulling out two Poké Balls. He then threw them upwards, saying, "Come on out, Minun and Sneasel!" The red and white orbs opened moments later, both Minun and Sneasel appearing in front of Hareta a second afterward.

Both Minun and Sneasel cheered at being let out as Hareta caught their Poké Balls, slipping them back into his pockets. They then ran over to the boy and he scooped them up into his arms, giving them a hug. He soon held them out and Minun asked, "(What are we going to do today, Hareta?)"

The raven-haired boy replied, "Well, we're gonna go see Gramps first. Dad said he mentioned that he would like to see what kind of data I have in my Pokédex at the moment, so I thought I'd go show him. After that… well, we'll figure it out as we go!"

Sneasel giggled, "(I like when we do that! It makes the day so much more interesting!)"

Hareta smiled and held them up towards his shoulders, both Pokémon leaping out of his arms and perching on them, Minun on his right and Sneasel on his left. He then said, "Well, let's get going, then!" He ran over to the front gate and used his arms to propel himself over it, landing on his feet on the sidewalk. He then started jogging down the street towards Route 201, both Minun and Sneasel gripping onto his jacket tightly. Even though it had only been three days since they got back from Johto, they were still excited about having a little time to relax before they set out on another adventure.

In what felt like no time at all, Hareta, Minun, and Sneasel left Route 201 and entered Sandgem Town. Hareta slowed down as he approached his grandfather's lab and knocked on the front door several times. For a few seconds, he heard the sound of rustling and muffled talking coming from the other side of the door before it opened. Mitsumi poked her head out, wearing an annoyed look on her face, but it eased off when she saw Hareta standing there. "Oh! Hello, Hareta. What's going on?" she asked, sounding slightly out of breath.

Hareta replied, "Dad told me the other day that Gramps wanted to look at my Pokédex. Since I was just thinking about it, I figured I'd stop by now and show him."

Mitsumi nodded, "I see. Well, come on in, then. Just watch your step; it's a little messy in here right now." She pushed her hand out, opening the door a little wider before pulling back inside. Hareta stepped inside after her, pulling the door closed behind him. He looked around and noticed a few scattered piles of paper along with some candy wrappers on the floor. Minun and Sneasel leapt off of his shoulders, going over to the wrappers on the floor and sniffing them, looking for leftover bits of food. Mitsumi spoke, bringing Hareta's attention back to her, "Professor Rowan is in the back. You can go ahead; I have to clean up this mess your father made."

As she crouched down to start gathering papers, Hareta offered, "Uh, do you want some help?"

Mitsumi replied, "That would be nice, seeing as your father is practically no help at all in an enclosed space." Hareta looked confused by her choice of words, but he figured she didn't mind him helping, so he bent down, grabbing some papers and a candy wrapper Minun had deemed to have nothing worthwhile in it.

After a couple of minutes, the lab was looking much cleaner than it did when Hareta had arrived. As he and Mitsumi set some reports down on the table, Professor Rowan and Kaisei walked out of the Professor's personal area. Professor Rowan was saying, "Really Kaisei, I could've easily gotten you something to eat. There was no need to go raiding my refrigerator just to satisfy your hunger. I doubt those sweets will hold you for long anyway."

Kaisei complained, "But… you heard my stomach, Professor! It needed something in it! I wasn't about to let it down! Besides, your whole fridge has nothing but sweets and candy in it. You didn't have to make such a big deal over me taking a few things out of it."

Professor Rowan replied, "If I hadn't asked Mitsumi to use her Infernape to restrain you, you would've kept going! Don't think I didn't see that look in your eyes!" Turning his attention away from his friend, he noticed Hareta and Mitsumi standing next to his table. He spoke, "Ah, hello Hareta. Decided to come visit, did you? And thank you for helping Mitsumi clean up the mess."

Hareta grinned, "No problem, Gramps!"

Kaisei glanced down as Plusle ran out of the adjacent room and over to Minun and Sneasel, eagerly greeting its fellow Cheering Pokémon. They both ran around a bit before running over to Kaisei and he scooped them up, saying, "Hey you two! I know you're happy to see each other again, but don't go making a mess in Professor Rowan's lab!" They both looked at each other and giggled happily.

Sneasel walked over to Hareta and tugged on the leg of his jeans. He looked down at her and smiled, bending down and picking her up. Professor Rowan noted, "I see Sneasel is still very fond of you, Hareta."

Hareta stood up with Sneasel in his arms and replied, "Yep! We're as close as ever."

Professor Rowan nodded and asked, "I assume my message found its way to you?"

Hareta looked up at him for a moment before he remembered, "Oh yeah! Dad told me the other night." He reached into his jeans pocket with his right hand and brought out his Pokédex, handing it to Professor Rowan.

The Professor replied, "Very good. This will just take a minute." He walked over to one of the computers in his lab and sat down on the chair in front of it. He hooked the Pokédex up to the machine with a cable and then typed in a few things on the keyboard. Within seconds, the computer started scanning the data contained in the Pokédex.

While the can was going on, Hareta walked over to the Professor and asked, "Hey Gramps, what happened to Jessie, James, and Meowth? Weren't they… helping you?"

Professor Rowan turned to look at him, saying, "That's correct, Hareta. They agreed to help me in the lab until they were ready to get back on their feet. They left around the time you were in Viridian City, saying they were going to look for a more fitting line of work. Before they left, I told them they could come back if they ever needed anything. I haven't seen them since."

Mitsumi came over and said, "That's actually part of the reason Professor Rowan wanted me to come back. He said he needed a little extra help around the lab."

Hareta nodded, "I see." He looked down at Sneasel, the Sharp Claw Pokémon looking up at him. It seemed she was disappointed that they had left too.

After a minute, Professor Rowan's computer beeped and they all looked at it. "The scan is complete. Let's take a look at the results," Professor Rowan said, scrolling through a list as Kaisei came over with Plusle and Minun, Minun leaping onto Hareta's shoulder. Professor Rowan soon spoke, "Between Johto and Kanto, you've certainly seen a lot of Pokémon, Hareta. There's even an entry for Ho-Oh here. You must have been lucky enough to see it when all those sightings were reported after that week of darkness."

Hareta scratched his head as he said, "I guess so. I don't remember seeing it, but maybe that's because I was so tired when the sun came back that I didn't even notice."

Mitsumi looked at him and asked, "You mean YOU were tired? What were you doing?"

Hareta looked at her and said, "Well, there were a bunch of these… dark creatures going around the Johto region, hunting others. Whenever they saw me, I either had to fight or run away from them. Either way, it wasn't easy."

Mitsumi asked, "Dark creatures?" Looking away, she held a hand up to her face, wondering, "Maybe the same things that were showing up all over Sinnoh?"

Professor Rowan spoke, "Well, whatever they were, I'm glad nothing happened to any of you." Looking back at his computer, he disconnected Hareta's Pokédex and handed it to the boy, who held it in his right hand and looked down at it. "You're doing very well on filling the National Pokédex, Hareta. What you've gathered so far should be a big help to my research," Professor Rowan said.

Hareta looked up at him and asked, "Your research?"

Kaisei nodded, "That's right. Professor Rowan specializes in Pokémon evolution, remember."

Mitsumi added, "It's like if you gave your Pokémon special training in order to overcome a certain obstacle in, say, battle. It's the main thing you focus on."

Her words got Hareta thinking, "_Special training? I've given my Pokémon that before… and I've had some too! Hey, that's an idea!_"

He slid his Pokédex into his jeans and started towards the door with Sneasel and Minun in tow. Mitsumi called after him, "Hareta, where are you going?!"

Hareta stopped in front of the door and turned back, saying, "With all this training talk, I feel like paying a visit to Iron Island to get some training in! I could probably use some right now!"

Professor Rowan asked, "Trying to keep your Pokémon in top form?"

Hareta shrugged, "Yeah, that too. Plus, I want to see Riley again!" Minun gave a happy exclamation at that while Sneasel looked up at Hareta curiously. He noticed the look and said to her, "You'll like Riley, Sneasel. He's a really nice guy!" Sneasel's face seemed to brighten at that.

Mitsumi sighed and smiled softly, "It's one great suggestion after another with you, as usual, of course."

Professor Rowan said, "I know it's not as much as a concern for you, seeing as you enjoy playing with the forest Pokémon, but remember not to neglect your own well-being. Be sure to train your own body as well, Hareta."

Hareta nodded, "I'll be sure to do that while I'm there, Gramps!"

Kaisei said, "Well, whatever you do, make sure you're home in time for dinner. Your mother said she's going to make something really good tonight!"

Hareta replied, "I will, Dad! Oh yeah, that reminds me… Mom said it's your turn to do the dishes tonight!" He then pushed the front door open and hurried down the path to Route 202, his father's loud groan following him out the door.

**Soon, on Iron Island…**

Riley was sitting at the table in Byron's cabin, flipping through the pages of the ancient journal while his Lucario meditated in the corner. Riley scanned the ancient writing on the pages, having become quite proficient in being able to determine what the symbols meant in the past few months.

After a few minutes, he got to the end of the pages he was on and looked up, thinking about all the information he had seen in the journal so far. "This Lyra Dia was quite knowledgeable in the ways of Aura. Everything in here, the training reports, the experimenting, the general knowledge that has likely been lost over time… It's all greatly contributed to my own understanding of Aura," he murmured to himself. Looking back down at the pages, he mused, "That one section in particular has been very helpful. It really explains why my own Aura was the way it was when I unleashed it." Crossing his arms atop the table, he said, "Come to think of it, I wonder how Hareta is doing. He must be finished with his journey in Johto by now."

He glanced over at his Lucario when he heard the Aura Pokémon grunt. Its eyes were still closed, but it was looking in the direction of the door. "_Someone or something is approaching,_" Riley realized. A minute passed in silence before Riley's Lucario slowly opened his eyes. Riley smiled, "Someone we know?" Lucario looked at him and smiled, nodding in confirmation.

A few seconds later, there was a knock on the door and Riley stood, walking over to the door and pulling it open. Looking down, he smiled, "Ah, hello Hareta! I was just thinking about you."

The boy returned the smile, "Hi, Riley! Did Byron tell you I was back?"

Riley chuckled, "I'm afraid not. Byron's had a few challengers to his Fortress of Steel the past few days, I know that much. I've seen them going into the mine to train for a rematch. I talked to a few, but I didn't help train with them like I did with you and Jun." He moved to the side while saying, "Come in." Hareta stepped inside, Minun and Sneasel jumping down from his shoulders and running over to Riley's Lucario. Hareta, meanwhile, set his backpack down on the floor and sat down at the table while Riley sat down across from him. The older Trainer then asked, "So, did you complete my request?"

Hareta thought for a moment before replying, "Oh yeah, I found out what that thing was! I actually found out what it was before I got to Blackthorn City!"

Riley tilted his head slightly, intrigued. "Oh?"

Hareta nodded, "Yeah! You want to see it?" Riley slowly nodded, wondering how Hareta could have it when he didn't have the duffel bag he was given. The boy stood up and took a few steps back from the table. He then held his right hand out in front of him, his thumb pointing parallel to the table. He then spoke, "Tsumugari!" As soon as he said that, the blue Glaive appeared in his hand!

Riley's eyes widened and he stood up at the sudden appearance, and even his Lucario looked up in surprise. "What… Hareta! What is this?!" Riley asked.

Hareta replied, "It's the Tsumugari! This is what that thing really looks like! I think it returned to normal when I used my Aura close to it. It's some kind of sword that was used by a goddess named Amaterasu and her son Chibiterasu a long time ago."

Riley sat back down, still surprised. "Amazing… So it really does exist…" he murmured.

Hareta heard him and, while setting Tsumugari down so it leaned against the table, asked, "What do you mean?"

Riley explained, "The Tsumugari is mentioned several times in my journal, and I remember reading about it elsewhere. The brother of the journal's owner was apparently being trained in using the Tsumugari."

Hareta asked, "Brother?" Riley nodded; Hareta then said, "That must be Grandpa Enta! Your journal must have belonged to his sister, Lyra!"

Riley asked, "Enta and Lyra? I remember seeing those names a few times… But how do you know those names, Hareta?"

The boy giggled, "Easy! I met them, or rather their Aura Spirits!"

Riley asked, "Aura Spirits?"

Hareta nodded, "Yeah, they're ghosts that an Aura user can create to continue living on even after death! After my friends and I arrived in Blackthorn City, I met their Aura Spirits and their dad, Hiori Dia, in the Dragon's Den and was trained to use my Aura and Tsumugari by them!"

Riley held his right hand to his head, resting his elbow on the table as he took it all in. "I've heard of powerful Aura Guardians being capable of living on even after death, but it's really true…? That's incredible…" he muttered. After a minute of silence, an idea came to him and he lowered his hand, looking directly at Hareta. "Hareta, were you really trained to use your Aura by these Aura Spirits?" he asked.

Hareta nodded, "Yeah, why?"

Riley stood up and said, "That answers my other question regarding your Aura training. I wanted to check on your progress when you got back, but after hearing that story, I want to see it firsthand. What do you say to a duel?"

Hareta looked up at Riley in surprise, "A duel?"

Riley replied, "It will not be a serious duel. I merely want to see how far you've progressed since you left. And as I told you, I am an Aura user myself. I have been training myself here. I think you will find that I am quite capable of holding my own. So what do you say?"

Hareta looked down, thinking about what Riley was asking for a moment. He then looked up and smiled, "Sounds like fun!"

Riley smiled back, "There's the Hareta I know. Follow me." After saying that, he walked towards the door, his Lucario standing up and following him. Hareta grabbed his backpack and sent Tsumugari away before following after them, Minun and Sneasel coming over and jumping up on his shoulders.

**Soon…**

Hareta and Riley stood across from each other, the two standing in the middle of the large, flat area on top of Iron Island, the same place where Hareta unleashed his Aura for the first time. Hareta's Empoleon, Lucario, Typhlosion, Sceptile, Minun, and Sneasel and Riley's Absol stood near the wall at the edge of the field, all of them eager to see what was going to happen. Riley's Lucario stood closer between the two humans, serving as kind of a referee, though he promised to only step in if either of them went too far. Minun stood near Sneasel with his electric pompoms in his paws, the two of them planning to throw a few cheers during the duel.

Riley spoke, "You may unleash your Aura whenever you are ready, Hareta."

The boy nodded, "Okay!" He brought his arms up close together in front of him and then quickly extended them out to his sides, a blue flame surrounding his body as his eyes took on the same color. He looked at Riley; the older Trainer simply raised his head and closed his eyes, a blue mist beginning to surround him. When he opened his eyes, Hareta saw that his eyes were the same color blue. Hareta didn't know what to think; he thought Riley's Aura would look the same as his own, like a flame. "Uh, are you sure you're going to be okay?" he asked.

Riley nodded, "Absolutely. Now come. Show me what you've learned!"

Hareta grinned, "Okay!" He brought his hands close together in a 'C' shape, forming an Aura Sphere between them. Riley smiled calmly when he saw this; Hareta had barely been able to form and hold an Aura Sphere last time he'd seen him. Even as Hareta finished forming a standard Aura Sphere, Riley did not move. Hareta hesitated to release it, but the look on Riley's face seemed to be telling him to use it. Hoping that the older man knew what he was doing, Hareta brought his hands forward, releasing the Aura Sphere from them and sending it straight towards Riley.

As the sphere came at him, Riley still did not move, mentally preparing himself. "_A little closer… closer…_" he thought. After the Aura Sphere passed his Lucario, Riley mentally shouted, "_Now!_" while crouching down on one leg, holding his right arm out in front of him. With his hand open, he stood up while raising his arm. Much to Hareta's surprise, as he did, a wall of ice that was the same light blue color as his Aura came up with him, forming a barrier in front and to the sides of him! The boy's Aura Sphere crashed into the ice wall, shattering it but being destroyed as well.

"Whoa!" Hareta exclaimed with wide eyes, his Pokémon looking surprised as well. The remains of the ice and the dust formed by the explosion of the Aura Sphere created a cover that temporarily hid Riley from view.

When the dust cleared and Riley could be seen again, Hareta could see that his Aura was shining brighter and actually seemed to be gathering around him, much different from his own Aura. Lowering his hand, Riley said to Hareta, "Nicely done, Hareta. I can already see you've learned much in our time apart." He then smiled, "That makes it okay to show you how much I know!" He bent over and held his arms underneath him, body tensing up as he focused. As Hareta and the Pokémon watched, his Aura soon surrounded him in a different way, a layer of ice forming over parts of his body that looked like armor. He then stood up straight, his head and parts of his arms and legs exposed, and said as he started forming an Aura Sphere in his right hand, "Now, come at me!" He then threw the Aura Sphere, which was still small, at Hareta.

Hareta grinned, "All right!" He held his arms in front of him, bringing them together in an 'X'-shape and causing his Aura to gather around them like a barrier. Riley's Aura Sphere hit Hareta's Aura and exploded, pushing the boy back slightly. He quickly recovered, though, and suddenly dashed towards Riley, looking to get up close and personal with him.

Riley held his right hand out, palm facing towards the ground, and said, "Better watch where you're going!" He then unleashed a stream of Aura into the ground and Hareta saw something coming up at the edge of his vision. He slowed down and planted his feet on the ground, sliding to the edge of where he could Riley's Aura as large ice pillars burst out of the ground. As Hareta stared up at them, Riley began to move, focusing his Aura into his legs to speed up his movements as he moved amongst the pillars he'd created.

Hareta focused as Minun and Sneasel threw him a few cheers, running into the collection of pillars and searching for Riley, though the Aura in the pillars made it hard to locate him as he kept moving from one pillar to the next. Hareta eventually came to a stop amongst the pillars and hunched over as he focused his Aura into his body. After a few moments, he held his arms out, hovering slightly above the ground as he released his Aura and breaking some of the pillars around him.

Almost immediately after he landed, he looked up to see Riley coming down at him with a kick. Hareta immediately held up his right arm to stop the kick, the impact surprising him a bit as it felt a bit cold to the touch. Riley pushed off of his arm with his foot, flipping back to land on his feet. As he stood up, Hareta focused a small amount of his Aura into his right fist and ran up to Riley. The older man braced himself as Hareta slammed his fist into the ice covering his chest. The boy paused for a moment before backing off, holding his right hand with his left hand. It wasn't that it hurt a lot; he was surprised by just how cold the ice was to the touch.

He didn't get a lot of time to ponder it before Riley dashed up to him and started attacking with a series of punches and kicks. He was fast, but Hareta's experience made it easy for him to deflect the attacks. After deflecting several series of hits, Hareta found an opening and stepped back, quickly focusing his Aura into his hands and holding them out before releasing it, his Aura emerging as a flame that pushed Riley backwards slightly.

After he stopped sliding, the older Trainer held his hands out in front of him with the open side down, the palms beginning to glow brighter. Aura ice crystals began to sprout out of the ground, the ice traveling straight towards Hareta. The boy responded by creating an Aura Sphere and launching it at the end of the trail before it could reach him, forming a small crater. He then looked back at Riley; this was getting exciting.

Their mock battle continued for some time, both Hareta and Riley showing off various the Aura skills they knew and their physical prowess, using a good portion of the field as they continued. Eventually, they got to the point where they were standing a short distance apart, facing each other while trying to catch their breaths. Riley's Lucario leapt forward at this, landing between the two and holding his paws out between them. Riley smiled as he stood up straight, "Good call, Lucario. I'm not sure we could've gone much longer anyway." His Lucario smiled up at him at that.

Hareta sighed and stood up straight, smiling at Riley, "Wow, Riley, that was really amazing. I had no idea you could do that with Aura."

Riley looked down at him and replied, "Well, not everybody can. That's not meant to be a boast; there are some things that can only be done if you have a specific Aura type."

Hareta looked confused, "Aura type?"

Riley nodded, "That's right. Since we last saw each other, I've learned that there are a few ways that Aura can differ for both humans and Pokémon." He held his right arm out to his side, gesturing beyond the field they were in as he said, "If you're interested, I can tell you more." Hareta glanced down, thinking for a moment before looking back up at him and nodding. Riley nodded back and, along with their Pokémon, the two Trainers started walking.

A couple of minutes later, Hareta, his Empoleon, and Lucario sat across from Riley and his Lucario, Minun and Sneasel sitting on Hareta's shoulders. Lyra's journal sat in front of Riley on the table, the older Trainer flipping through the pages to find the section he was searching for. After a few seconds, he hesitated at a page and then stopped before saying, "Here it is. This is the section that talks about the different Aura types."

Hareta asked, "How many are there?"

Riley answered, "Three are recorded here. We'll start off simple. The first recorded Aura type is the Fire Aura."

Hareta cocked his head, "Fire Aura?"

Riley nodded, "Yes. Of the three Aura types, the Fire Aura is perhaps the most well-known, even if one is not aware that there are different Aura types. Your Aura is an example of a Fire Aura, Hareta. When it is unleashed, it has the appearance of a flame, burning from deep within you. It is obviously not a fire like you would make at night, but it looks and behaves very similarly. When using it to attack, it can be spread the same way a fire might spread and even take on the appearance of a Pokémon's Fire-type attacks. It can even be used to heal, burning wounds and other damages away and increasing the speed of someone's recovery so to speak."

Hareta held out his right hand and looked down at it, "I've actually made use of that a few times. So that's how it works…" Setting his hand down on the table, he looked back up at Riley and asked, "What kind of Aura do you have, Riley?"

The older Trainer replied, "Mine is an Ice Aura. As you've seen, it's quite different from the Fire Aura. Instead of having the appearance of fire, it appears more like real ice, covering the user in an armor-like covering of ice when it's fully unleashed. The user can choose to spread it like the Fire Aura, but ice can also be created and used in other ways, and it doesn't have the healing capabilities of the Fire Aura. You could perhaps cover a surface wound under a layer of ice, but it won't heal any faster."

Hareta shivered, "Brr… I'm getting cold just thinking about what that would be like." He then had a thought and asked, "Hey, even though they're different, the Fire and Ice Auras have other similarities besides the whole spreading thing, right? Like, uh, Aura Spheres and stuff?"

Riley nodded, "Yes, that's correct. While some Aura skills are better learned by a particular type of Aura user, skills such as using Aura Sphere are considered standard for Fire, Ice, and Lightning Aura users."

Hareta asked, "So the last Aura is called Lightning Aura? How do you know if someone has it?"

Riley answered, "Like with any Aura type, it depends on how much Aura is being unleashed by someone. Fire Aura usually first appears as fire coming from someone's hands, the air begins to cool around someone who is beginning to unleash their Ice Aura, and Lightning Aura… well, simply put, it's appears as though electricity is traveling across someone's body, though according to this, it's more likely to be found surrounding the arms and legs than anywhere else. And since it's like real lightning, it has electric properties and temporarily become stronger if a local source of electricity is absorbed."

Hareta nodded and looked down at the table in thought. He thought about his journey in Johto, his rushed Aura and sword training, and the first real enemy he'd had to use his Aura against. Remembering Faust, he looked back up at Riley and said, "Hey Riley, I have another question. Is it possible for Aura to be other colors? Like black, for instance?"

Riley thought for a moment before replying, "Well, yes, it is possible, Hareta. There's some slight history written here in this journal, but I've also found some other literature on the history of Aura. Unfortunately, some of the details are not entirely clear, but what I found was informative."

Hareta asked, "Like what?"

Riley answered, "As far back as I can tell, since ancient times, Aura users originally only had blue Auras, much like we do. At some point, however, some sort of crystal was discovered in a region that would go on to change that. I did not recognize the name of the region, though I'm certain its name has changed after so many years, but anyway, the ones who discovered this crystal were themselves Aura users. When they came into contact with the crystal, it supposedly corrupted them, turning their Auras from blue to black."

Hareta looked a bit nervous, as did Sneasel and Minun while Empoleon and Lucario appeared to show no signs of apprehension. "What happened to them?" Hareta asked.

Riley replied, "Because their Auras were corrupted, they themselves were corrupted. Having been turned into the opposite of what they once were, I'm sure you can guess that they turned their backs on everything they once knew and believed in. From what I can tell, they and others who followed them were eventually stopped, but by then, the effects of their corruption had changed the balance of Aura itself. As I said, Aura was strictly blue before. By the time the black Aura users had been stopped, Aura users possessing many different colors had made themselves known in the efforts to stop the threat. From then on, it became possible for anyone who felt a strong connection to Aura to learn how to use it, regardless of the color of their Aura."

Hareta asked, "Wait, did the black Aura users change the color of other Auras, or were there always different colors?"

Riley answered, "Other colors of Aura have always existed. However, up until that time, it seems that the only ones allowed to use Aura had to possess a strong connection to it and have a blue Aura. Other colors were seemingly deemed to have been 'tainted', essentially implying that, had they gone on to learn how to use Aura, they would've corrupted or otherwise destroyed themselves. They were forbidden to learn, but it wouldn't surprise me if some tried to do it in secret. My assumption is that, when the black Aura was threatening the land, the non-blue Aura users proved that they could be valuable allies and managed to change things. I read about all of this in a fairly old book, so it's possible not all of it is true, but that seems like the most logical explanation."

Hareta nodded, "I see…" He tilted his head down slightly, looking at the table again.

Riley noticed the look on the younger Trainer's face. He had seen a similar look the first time he'd met him, when he'd suggested that Hareta not use his Piplup for his training on Iron Island. The look on his face as he considered those words spoke volumes about his dedication to his Pokémon and desire to learn. He could tell Hareta had learned quite a bit about Aura, yet was still eager to learn more if he was allowed to.

Flipping the journal in front of him closed, Riley rested his elbows on the table at its sides, his fingers crossed together under his chin as he spoke, "Hareta," he paused to smile slightly as the boy looked up at him curiously, "I have told you what I have learned since you returned to Johto, but I am curious just how much you have learned in that time, especially from your meetings with the Aura Spirits. And I have a feeling I still have a few things I can teach you." He lowered his hands down onto the table, "Would you like to train with me and my Lucario again? And this time, your Lucario can learn alongside you instead of teaching you." He smiled a bit wider as he saw an excited look grow on Hareta's face, his Lucario also looking happy at his words. "_I'll take that as a 'yes',_" he thought to himself.

**Meanwhile…**

Charon sat in his chair with his back facing towards his desk, a badly dented computer monitor sitting on top of it. He found it embarrassing, really, that he was using something so old, especially in a region of the world that was so technologically advanced, but until he started terrorizing the world and getting all the money he deserved, he would have to make do with the outdated-looking machine. And, according to his new 'business partner', it was better that he was using it; less chance of him being discovered, apparently.

Charon spoke, "So we are in agreement, then?"

A voice came from the computer monitor, the voice having a Russian accent to it, "Yes, ze terms are acceptable. Ve vill both benefit nicely from this business… comrade."

Charon turned his chair around so he was facing his desk, "Good. When will the rest of your men arrive?"

The voice responded, "My men are still cleaning up after the… unexpected events I described to you, and I still cannot track down the squads zat have gone missing as result of said events. Zey vill be along, but not as soon as you are requesting."

Charon sighed, but said, "Very well. I'll make do with what you've sent over. They'll be stationed on my new aircraft once it's ready for launch."

The voice answered, "No! Zis is very risky deal I am making with you, Charon; if vord of zis gets out… My men are not for your use until you produce results, and I vill be expecting first payment not long afterwards if you vish to continue our agreement."

Charon sighed, "…As you wish. They'd just better be as good as you're making them out to be."

The voice replied, "Zat will largely depend on your cooperation, comrade. You vill have chance to prove yourself to me soon, however. Have you received the other part of my 'donation' yet?"

Charon answered, "Yes, it just arrived. I have a scientist who's confident that he can make good use of it. He's confident that there is a way to work around that disgusting identification system that's becoming so commonplace nowadays that will allow them to be used."

The voice said, "If you can provide proof of this, then I vill allow you full use of my men, so long as I am compensated for."

Charon nodded, "You will be."

The voice warned, "Don't disappoint me."

As the monitor's screen began to dim, Charon smirked, "I won't."

* * *

><p>Well... at long last, the next chapter of "The Shadow Flames" has been posted. Seriously, this was sitting for months unfinished and I didn't feel ready to post it when I did finish it, so... Well, it's not going to make up for how long it took to post it, but I hope, for what it is, it's a good read.<p>

I don't have much to say here since not a lot happens. This and the first chapter are slow (that might be part of the reason I was reluctant to put it up, since it feels like more should have happened, but I couldn't do it), but next chapter will have more action and start to move through the story a bit faster so we can get out of Sinnoh and move to Orre, where the bulk of the story will happen.

If there's one thing I will say, this chapter was a good way to show everyone what RandomPerson422 and I have been working on in regards to what we're doing with Aura. All the Aura types and how they work are all things we've come up with together. Unfortunately, I seem to have lost the note containing everything we came up with, so I really hope I remembered everything.

So... yeah, that's about it. I apologize for the long wait and I hope I will be able to update this story more frequently in the future!

The owner of the voice at the end belongs to RandomPerson422.


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